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John Barnard

Publications and source records attributed to John Barnard.

18 recordsLinked to original sources
PubMed2025

Genetic architecture and analysis practices of circulating metabolites in the NHLBI Trans-Omics for Precision Medicine Program.

Circulating metabolite levels partly reflect the state of human health and diseases and can be impacted by genetic determinants. Hundreds of loci associated with circulating metabolites have been identified; however, most findings focus on predominantly European ancestry or single-study analyses. Leveraging the rich metabolomics resources generated by the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) Program, we harmonized and accessibly cataloged 1,729 circulating metabolites among 25,058 ancestrally diverse samples. From our comparison of multiple methods, we provided a set of reasonable strategies for outlier and imputation handling to process metabolite data and show that inverse normalization by study and half-minimum imputation provide mostly similar results for pooled or meta-analysis. Following the practical analysis framework, we further performed a genome-wide association analysis on 1,135 selected metabolites using whole-genome sequencing data from 16,359 individuals passing the quality-control filters and discovered 1,775 independent loci associated with 667 metabolites. Among 160 unreported locus-metabolite pairs, we identified associations with loci locating within previously implicated metabolite-associated genes, as well as associations with loci locating in genes such as GAB3 and VSIG4 (located on the X chromosome) that may play a role in metabolic regulation. In the sex-stratified analysis, we revealed 85 independent locus-metabolite pairs with evidence of sexual dimorphism, which were located in well-known metabolic genes such as FADS2, D2HGDH, SUGP1, and UGT2B17, strongly supporting the importance of exploring sex difference in the human metabolome. Taken together, our study depicted the genetic contribution to circulating metabolite levels, providing additional insight into the understanding of human health.

Humans↗
PubMed2006

Analysis of incomplete longitudinal binary data using multiple imputation.

We propose a propensity score-based multiple imputation (MI) method to tackle incomplete missing data resulting from drop-outs and/or intermittent skipped visits in longitudinal clinical trials with binary responses. The estimation and inferential properties of the proposed method are contrasted via simulation with those of the commonly used complete-case (CC) and generalized estimating equations (GEE) methods. Three key results are noted. First, if data are missing completely at random, MI can be notably more efficient than the CC and GEE methods. Second, with small samples, GEE often fails due to 'convergence problems', but MI is free of that problem. Finally, if the data are missing at random, while the CC and GEE methods yield results with moderate to large bias, MI generally yields results with negligible bias. A numerical example with real data is provided for illustration.

Clinical Trials as Topic↗
PubMed2006

Evaluation of transgenic 'Chardonnay' (Vitis vinifera) containing magainin genes for resistance to crown gall and powdery mildew.

Magainins, short peptides with broad-spectrum antimicrobial activity in vitro, were assayed for their ability to confer resistance to pathogens in transgenic grapevines. Embryogenic cell suspensions of 'Chardonnay' (Vitis vinifera L.) were co-transformed by microprojectile bombardment with a plasmid carrying the npt-II gene and a second plasmid harboring either a natural magainin-2 (mag2) or a synthetic derivative (MSI99) gene. Magainin genes and the marker gene were driven by Arabidopsis ubiquitin-3 and ubiquitin-11 promoters, respectively. A total of 10 mag2 and 9 MSI99 regenerated lines were studied by Southern blot hybridization, which showed 1-6 transgene integration events into the plant genome. Semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) revealed a variable range in transcription levels among mag2 and MSI99 lines. A positive correlation between number of integration events and transcription level was observed (p<0.05). Plants were acclimated and challenged in the greenhouse with either Agrobacterium vitis strains (bacterial crown gall pathogen) at 10(8) cfu/ml or Uncinula necator (fungal powdery mildew pathogen) at 10(5) conidia/ml for evaluation of disease resistance. A total of 6 mag2 and 5 MSI99 lines expressing the antimicrobial genes exhibited significant reductions of crown gall symptoms as compared to non-transformed controls. However, only two mag2 lines showed measurable symptom reductions in response to U. necator, but not strong resistance. Our results suggest that the expression of magainin-type genes in grapevines may be more effective against bacteria than fungi. Additional strategies to enhance transgene expression and the spectrum of resistance to grape diseases are suggested.

Amino Acid Sequence↗
PubMed2005

Atherosclerosis susceptibility loci identified from a strain intercross of apolipoprotein E-deficient mice via a high-density genome scan.

OBJECTIVE: Apolipoprotein (apo) E-deficient mice are hypercholesterolemic and develop atherosclerosis on low-fat chow diets; however, the genetic background strain has a large effect on atherosclerosis susceptibility. This study aimed to determine the genetic regions associated with strain effects on lesion area. METHODS AND RESULTS: We performed a strain intercross between atherosclerosis sensitive DBA/2 and atherosclerosis resistant AKR apoE-deficient mice. Aortic root lesion area, total cholesterol, body weights, and complete blood counts were ascertained for 114 male and 95 female F2 progeny. A high-density genome scan was performed using a mouse single nucleotide polymorphism chip yielding 1967 informative polymorphic markers. Quantitative trait locus (QTL) statistical analyses were performed. Novel loci associated with lesion or log lesion area were identified for the female and male F2 cohorts. The atherosclerosis QTLs in female mice reside on chromosomes 15, 5, 3, and 13, and in male mice on chromosomes 17, 18, and 2. QTL were also identified for body weight, total cholesterol, and blood count parameters. CONCLUSIONS: Loci were identified for atherosclerosis susceptibility in a strain intercross study. The identity of the responsible genes at these loci remains to be determined.

Animals↗
PubMed2005

A common inversion under selection in Europeans.

A refined physical map of chromosome 17q21.31 uncovered a 900-kb inversion polymorphism. Chromosomes with the inverted segment in different orientations represent two distinct lineages, H1 and H2, that have diverged for as much as 3 million years and show no evidence of having recombined. The H2 lineage is rare in Africans, almost absent in East Asians but found at a frequency of 20% in Europeans, in whom the haplotype structure is indicative of a history of positive selection. Here we show that the H2 lineage is undergoing positive selection in the Icelandic population, such that carrier females have more children and have higher recombination rates than noncarriers.

Chromosome Inversion↗
PubMed2005

Differential regulation of cyclooxygenase-2 in nontransformed and ras-transformed intestinal epithelial cells.

To determine signaling pathways responsible for modulation of COX-2 expression in nontransformed and transformed epithelial cells, we studied a rat intestinal epithelial (RIE) cell line expressing constitutively active Ras and RhoA. Expression of COX-2 protein was higher in RIE-RhoA(63L) (four-fold) and RIE-Ras(12V) (seven-fold) cells than in parental cells. Prior work suggests that Ras hyperactivity induces the expression of transforming growth factor (TGF)beta and increases epidermal growth factor (EGF)-related peptide signaling-possible mechanisms for increased COX-2 expression. Expression of COX-2 was stimulated by TGFbeta and TGFalpha in RIE and RIE-Rho(63L) cells, but not further stimulated in RIE-Ras(12V) cells. PD153035, an inhibitor of EGF receptor tyrosine kinase, and PD98059, an inhibitor of Erk, attenuated COX-2 expression in RIE and RIE-RhoA(63L). However, the high levels of COX-2 expression in RIE-Ras(12V) cells were not inhibited by either compound. Titration with a pan-neutralizing anti-TGFbeta antibody did not decrease COX-2 in RIE-Ras(12V) cells, even with concurrent EGFR inhibition. Thus, stimulation of the EGF receptor is important in the modulation of COX-2 expression in nontransformed RIE and RIE-RhoA(63L) cells. In Ras-transformed cells, signaling by additional Ras effector pathways, perhaps the RhoA pathway, must be invoked. Identification of these pathways is critical for therapeutic manipulation of COX-2 expression.

Animals↗
PubMed2004

Recombination rate and reproductive success in humans.

Intergenerational mixing of DNA through meiotic recombinations of homologous chromosomes during gametogenesis is a major event that generates diversity in the eukaryotic genome. We examined genome-wide microsatellite data for 23,066 individuals, providing information on recombination events of 14,140 maternal and paternal meioses each, and found a positive correlation between maternal recombination counts of an offspring and maternal age. We postulated that the recombination rate of eggs does not increase with maternal age, but that the apparent increase is the consequence of selection. Specifically, a high recombination count increased the chance of a gamete becoming a live birth, and this effect became more pronounced with advancing maternal age. Further support for this hypothesis came from our observation that mothers with high oocyte recombination rate tend to have more children. Hence, not only do recombinations have a role in evolution by yielding diverse combinations of gene variants for natural selection, but they are also under selection themselves.

Adolescent↗
PubMed2004

Quantification of substratum contact required for initiation of Colletotrichum graminicola appressoria.

Colletotrichum graminicola, like many plant pathogenic fungi develop appressoria on germling apices, to facilitate penetration of their host. Induction of these structures occurs after contact with the host surface has been established by the germling. Surface contact and subsequent development of appressoria by germlings of C. graminicola was assessed using interference-reflection microscopy (IRM) and microfabricated pillared silicon substrata. Observations with IRM revealed that under low nutrient conditions, 90% of the germlings developed appressoria once they established 4.5 microm of continuous contact with the substratum. Substrata bearing pillars < or =5 microm in width supported < or =10% appressoria; however, as pillar width was increased the percentage of appressoria formed increased in a sigmoid fashion to a maximum of 80%. The percentage of appressoria produced experimentally on these surfaces was compared to data sets generated from a model designed to calculate the probability of appressorium development on similar pillar arrays at various germ tube contact lengths. These results indicate that germ tubes of C. graminicola require more than 4microm of continuous contact with a hydrophobic substratum for induction of appressoria.

Cell Wall↗
PubMed2004

Raf and RhoA cooperate to transform intestinal epithelial cells and induce growth resistance to transforming growth factor beta.

Although unregulated activation of the Ras/Raf/mitogen-activated protein kinase kinase/Erk signaling pathway is believed to be a central mechanism by which many cell types undergo oncogenic transformation, recent studies indicate that activation of Raf kinase by oncogenic Ras is not sufficient to cause tumorigenic transformation in intestinal epithelial cells. Thus, identification of signaling proteins and pathways that interact with Raf to transform intestinal epithelial cells may be critical for understanding aberrant growth control in the intestinal epithelium. Functional interactions between Raf and the small GTPase RhoA were studied in RIE-1 cells overexpressing both activated Raf(22W) and activated RhoA(63L). Double transfectants were morphologically transformed, formed colonies in soft agar, grew in nude mice, overexpressed cyclin D1 and cyclooxygenase-2 (COX-2), and were resistant to growth inhibition by transforming growth factor (TGF) beta. RIE-Raf and RIE-RhoA single transfectants showed none of these characteristics. Expression of a dominant-negative RhoA(N19) construct in RIE-Ras(12V) cells was associated with markedly reduced COX-2 mRNA, COX-2 protein, and prostaglandin E2 levels when compared with RIE-Ras(12V) cells transfected with vector alone. However, no change in transformed morphology, growth in soft agar, cyclin D1 expression, TGFalpha expression, or TGFbeta sensitivity was observed. In summary, coexpression of activated Raf and RhoA induces transformation and TGFbeta resistance in intestinal epithelial cells. Although blockade of RhoA signaling reverses certain well-described characteristics of RIE-Ras cells, it is insufficient to reverse the transformed phenotype and restore TGFbeta sensitivity. Blockade of additional Rho family members or alternate Ras effector pathways may be necessary to fully reverse the Ras phenotype.

Alkyl and Aryl Transferases↗
PubMed2003

Growth inhibitory signalling by TGFbeta is blocked in Ras-transformed intestinal epithelial cells at a post-receptor locus.

The transforming growth factor beta (TGFbeta) family of growth regulatory peptides plays an important role in the regulation of gastrointestinal epithelial cell homeostasis. Loss of growth inhibitory signalling by TGFbeta is common in the context of Ras-transformation and it has been hypothesized that loss of TGFbeta receptor II (TGFbetaRII) expression accounts for the emergence of TGFbeta resistance. Here we examine the functional significance of reduced TGFbetaRII expression in intestinal epithelial cells transformed by oncogenic Ras. TGFbeta-induced signalling events downstream of TGFbetaRII were examined in Ras-transformed RIE-1 cells (RIE-Ras) and compared to the parental RIE-1 line. RIE-Ras cells were resistant to growth inhibition by TGFbeta. Neither overexpression of TGFbetaRII in RIE-Ras cells nor expression of constitutively active TGFbetaRI restored sensitivity to TGFbeta. TGFbeta-mediated phosphorylation of Smad2 occurred in TGFbeta-resistant RIE-Ras cells, as well as other TGFbeta-resistant cells lines (HT-29, SW620) expressing low levels of TGFbetaRII. Nuclear translocation of Smad2 and Smad4 occurred equally in RIE-Ras and parental RIE cells. The activity of TIEG2, a TGFbeta-inducible SP1-like transcription factor, was reduced in RIE-Ras cells, implying that resistance in Ras-transformed RIE cells occurs by a transcriptional mechanism.

Active Transport, Cell Nucleus↗
PubMed2002

A high-resolution recombination map of the human genome.

Determination of recombination rates across the human genome has been constrained by the limited resolution and accuracy of existing genetic maps and the draft genome sequence. We have genotyped 5,136 microsatellite markers for 146 families, with a total of 1,257 meiotic events, to build a high-resolution genetic map meant to: (i) improve the genetic order of polymorphic markers; (ii) improve the precision of estimates of genetic distances; (iii) correct portions of the sequence assembly and SNP map of the human genome; and (iv) build a map of recombination rates. Recombination rates are significantly correlated with both cytogenetic structures (staining intensity of G bands) and sequence (GC content, CpG motifs and poly(A)/poly(T) stretches). Maternal and paternal chromosomes show many differences in locations of recombination maxima. We detected systematic differences in recombination rates between mothers and between gametes from the same mother, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.

Base Sequence↗
PubMed2002

A new statistical method for testing hypotheses of neuropsychological/MRI relationships in schizophrenia: partial least squares analysis.

We applied partial least squares (PLS) as a novel multivariate statistical technique to examine neuropsychological correlates of magnetic resonance imaging (MRI) measures of brain volumes in a well studied sample of 15 male patients with chronic schizophrenia. In the current study, because the total number of measures far surpassed the total number of subjects, extant multivariate techniques such as canonical correlation could not be used to examine relationships among simultaneous measures of MRI and neuropsychology. Moreover, because MRI measures were expected to be highly inter-correlated, as would be neuropsychological test scores, extant multivariate statistical techniques would be substantially limited because they typically assume statistical independence among sets of measures. PLS, on the other hand, proved to be especially well suited to examining the relationships among function and anatomy measures in this sample, where statistically significant relationships were demonstrated that were entirely consistent with prior studies using univariate correlation techniques. In particular, statistically significant relationships emerged among sets of MRI temporal lobe measures and neuropsychological tests of verbal memory and categorization as well as among MRI frontal measures and neuropsychological tests of working memory.

Adult↗
PubMed2002

Spatial and object working memory impairments in schizophrenia patients: a Bayesian item-response theory analysis.

This study reports evidence that schizophrenia patients are significantly impaired in both spatial and object (shape) working memory. A 3-s delay between exposure and recall of targets was used and Bayesian item-response theory was applied to compensate for the tasks' differential difficulty while simultaneously taking account of missing data from participant attrition. Weaker evidence was found that in schizophrenia both domains are equally impaired on average, that spatial and object working memory appear to be more highly correlated with each other in the schizophrenia population than in the normal population, and that schizophrenia patients show greater variability in spatial than object working memory performance.

Adult↗
PubMed2002

Histopathology of ulcerative colitis in initial rectal biopsy in children.

Definitive histologic diagnosis of ulcerative colitis relies upon mucosal architectural distortion and inflammation in the appropriate clinical setting. Although crypt branching, atrophy, and loss are usually present in first biopsies from adults with ulcerative colitis, it has been our impression that features of chronicity are often lacking in first biopsies from children. To test this hypothesis, initial rectal biopsies and follow-up biopsies and/or colonic resections from 53 children (age 15 months to 17 years) and 38 adults (age 21-76 years) with ulcerative colitis were examined in a blinded fashion for villiform surface, crypt atrophy, branching crypts, lamina propria inflammation, crypt abscesses, cryptitis, and basal plasma cells. Mucosal architecture was classified as normal, focally abnormal, or diffusely abnormal. Medical records were reviewed for confirmatory evidence of ulcerative colitis and for duration of symptoms before biopsy. In 87 of 91 biopsies, the lamina propria contained a mixed inflammatory infiltrate. Crypt abscesses and cryptitis were common in both groups. Initial biopsies from children were less likely to show diffuse architectural abnormalities (17 of 53, 32.1%) compared with biopsies from adults (22 of 38, 57.9% p <0.05). Duration of symptoms before diagnosis was significantly shorter in children (mean 17.5 weeks) compared with adults (mean 54.9 weeks). In summary, initial rectal biopsies from children with ulcerative colitis are less likely to show diagnostic mucosal architectural distortion than biopsies from adults. This difference may be related to a shorter duration of symptoms before biopsy.

Adolescent↗